In a time when the role of science in society is under threat, this book provides a timely and accessible text that can be used to learn or teach both the theory and practices of science, and how they are interconnected. The first chapters introduce the major approaches to the philosophy of science using simple language and examples that are easy to understand. The chapters that follow build on philosophy of science to explain science practices such as publication, bibliometrics, experiments, the use of statistics, research ethics, and the academic career. The book emphasizes how and why science is the most reliable source of knowledge and how society is dependent on science to make informed decisions. It primarily targets science students but is also accessible to general readers interested in understanding how science works. It is ideal as a textbook for intermediate-advanced students majoring in any science (or engineering) subject.

The interactions between phytophagous insects and their host plants show a strong trend toward specialization. However, the reasons behind this trend remain largely unclear, at both the evolutionary and mechanistic level. One possible explanation is an increased energy expenditure for digesting and metabolizing more challenging hosts included in a broader host repertoire, which may reduce the energy available for other processes such as growth and development (“metabolic load hypothesis”). Differences in the performance across various hosts could reflect such costs. Using the polyphagous Polygonia c-album (comma butterfly), we tested whether observed performance differences can be linked to variation in the energetic requirements. For this, we measured the metabolic rate of larvae feeding on three different host plants and converted it into the amount of CO₂ produced per gram of mass gain (“growth cost”) to assess how much energy is allocated to growth vs. digestion and assimilation. The metabolic rate of larvae feeding on a chemically more challenging plant (Ribes uva-crispa) was similar to that of individuals on the host supporting the highest growth rate (Urtica dioica). However, larvae on Ribes uva-crispa exhibited a higher energy demand per unit of growth and a lower growth rate, indicating a different energy allocation in growing larvae than when they were reared on a chemically less challenging plant. Our findings suggest that energy expenditure for digesting different hosts varies and can have direct consequences for larval performance. This indicates that the trend toward ecological specialization may, at least partly, be driven by selection to reduce the energetic costs for detoxification and digestion, in support of the metabolic load hypothesis.

Evolutionary changes in geographic distribution and larval host plants may promote the rapid diversification of montane insects, but this scenario has been rarely investigated. We studied the rapid radiation of the butterfly genus Colias, which has diversified in mountain ecosystems in Eurasia, Africa, and the Americas. Based on a data set of 150 nuclear protein-coding genetic loci and mitochondrial genomes, we constructed a time-calibrated phylogenetic tree of Colias species with broad taxon sampling. We then inferred their ancestral geographic ranges, historical diversification rates, and the evolution of host use. We found that the most recent common ancestor of Colias was likely geographically widespread and originated ~3.5 Ma. The group subsequently diversified in different regions across the world, often in tandem with geographic expansion events. No aspect of elevation was found to have a direct effect on diversification. The genus underwent a burst of diversification soon after the divergence of the Neotropical lineage, followed by an exponential decline in diversification rate toward the present. The ancestral host repertoire included the legume genera Astragalus and Trifolium but later expanded to include a wide range of Fabaceae genera and plants in more distantly related families, punctuated with periods of host range expansion and contraction. We suggest that the widespread distribution of the ancestor of all extant Colias lineages set the stage for diversification by isolation of populations that locally adapted to the various different environments they encountered, including different host plants. In this scenario, elevation is not the main driver but might have accelerated diversification by isolating populations.

Quantifying the tempo and mode via modern phylogenetic comparative methods can provide key insights into how selection and constraints shape trait evolution on a macroevolutionary time scale. Here, we elucidate the evolution of hibernation (winter) diapause, a complex and defining life-history trait that allows temporal escape from harsh winters in temperate regions for many insects, including our model system, butterflies. Butterflies can diapause in all major life stages, and the availability of global-scale phylogenies makes them an ideal model system for studying diapause evolution. First, using a thorough literature survey, we scored the developmental stage of hibernation diapause (egg, larva, pupa, adult) vs. absence of diapause. We find that larval diapause is most common, while pupal, egg, and adult diapause are relatively rare. Next, we determined that the loss of diapause occurred at a much higher rate and that gains primarily occurred from the non-diapause state. While ancestral state estimation at deeper nodes remained uncertain, we found consistent patterns for some families and strong evidence for extensive convergence in diapause evolution. Contrary to expectations, we find no support for increased gain of diapause during the Eocene–Oligocene glaciation (~35 million years ago). Overall, the evolution of diapause in butterflies has a complex history, has evolved convergently, and has likely predated the major glaciation event consistent with the deep history of diapause evolution in insects. This study advances our understanding of the evolution of a complex and important life-history trait and establishes a macroevolutionary foundation for future studies on the ultimate and proximate basis of diapause evolution.

Comparative analyses of gene birth–death dynamics have the potential to reveal gene families that played an important role in the evolution of morphological, behavioral, or physiological variation. Here, we used whole genomes of 30 species of butterflies and moths to identify gene birth–death dynamics among the Lepidoptera that are associated with specialist or generalist feeding strategies. Our work advances this field using a uniform set of annotated proteins for all genomes, investigating associations while correcting for phylogeny, and assessing all gene families rather than a priori subsets. We discovered that the sizes of several important gene families (e.g. those associated with pesticide resistance, xenobiotic detoxification, and/or protein digestion) are significantly correlated with diet breadth. We also found 22 gene families showing significant shifts in gene birth–death dynamics at the butterfly (Papilionoidea) crown node, the most notable of which was a family of pheromone receptors that underwent a contraction potentially linked with a shift to visual-based mate recognition. Our findings highlight the importance of uniform annotations, phylogenetic corrections, and unbiased gene family analyses in generating a list of candidate genes that warrant further exploration.

Generalist plant-feeding insects are characterised by a broad host repertoire that can comprise several families or even different orders of plants. The genetic and physiological mechanisms underlying the use of such a wide host range are still not fully understood. Earlier studies indicate that the consumption of different host plants is associated with host-specific gene expression profiles. It remained, however, unclear if and how larvae can alter these profiles in the case of a changing host environment. Using the polyphagous comma butterfly (Polygonia c-album) we show that larvae can adjust their transcriptional profiles in response to a new host plant. The switch to some of the host plants, however, resulted in a larger transcriptional response and, thus, seems to be more challenging. At a physiological level, no correspondence for these patterns could be found in larval performance. This suggests that a high transcriptional but also phenotypic flexibility are essential for the use of a broad and diverse host range. We furthermore propose that host switch tests in the laboratory followed by transcriptomic investigations can be a valuable tool to examine not only plasticity in host use but also subtle and/or transient trade-offs in the evolution of host plant repertoires.

The genetic components of the circadian clock have been implicated as involved in photoperiodic regulation of winter diapause across various insect groups, thereby contributing to adaptation to adverse seasonal conditions. So far, the effects of within-population variation in these genes have not been well explored. Here, we present an experimental test of the effects of within-population variation at two circadian genes, timeless and period, on photoperiodic responses in the butterfly Pararge aegeria. While nonsynonymous candidate SNPs in both of these genes have previously shown to be associated with diapause induction on a between-population level, in the present experiment no such effect was found on a within-population level. In trying to reconcile these results, we examine sequence data, revealing considerable, previously unknown protein-level variation at both timeless and period across Scandinavian populations, including variants unique to the population studied here. Hence, we hypothesize that these variants may counteract the previously observed diapause-averting effect of the candidate SNPs, possibly explaining the difference in results between the experiments. Whatever the cause, these results highlight how the effects of candidate SNPs may sometimes vary across genetic backgrounds, which complicates evolutionary interpretations of geographic patterns of genetic variation.

Photoperiod is a common cue for seasonal plasticity and phenology, but climate change can create cue-environment mismatches for organisms that rely on it. Evolution could potentially correct these mismatches, but phenology often depends on multiple plastic decisions made during different life stages and seasons that may evolve separately. For example, Pararge aegeria (Speckled wood butterfly) has photoperiod-cued seasonal life history plasticity in two different life stages: larval development time and pupal diapause. We tested for climate change-associated evolution of this plasticity by replicating common garden experiments conducted on two Swedish populations 30 years ago. We found evidence for evolutionary change in the contemporary larval reaction norm-although these changes differed between populations-but no evidence for evolution of the pupal reaction norm. This variation in evolution across life stages demonstrates the need to consider how climate change affects the whole life cycle to understand its impacts on phenology.

In this study, we investigated whether patterns of gene expression in larvae feeding on different plants can explain important aspects of the evolution of insect-plant associations, such as phylogenetic conservatism of host use and re-colonization of ancestral hosts that have been lost from the host repertoire. To this end, we performed a phylogenetically informed study comparing the transcriptomes of 4 nymphalid butterfly species in Polygonia and the closely related genus Nymphalis. Larvae were reared on Urtica dioica, Salix spp., and Ribes spp. Plant-specific gene expression was found to be similar across butterfly species, even in the case of host plants that are no longer used by two of the butterfly species. These results suggest that plant-specific transcriptomes can be robust over evolutionary time. We propose that adaptations to particular larval food plants can profitably be understood as an evolved set of modules of co-expressed genes, promoting conservatism in host use and facilitating re-colonization. Moreover, we speculate that the degree of overlap between plant-specific transcriptomes may correlate with the strength of trade-offs between plants as resources and hence to the probability of colonizing hosts and complete host shifts.

Diapause is a common adaptation for overwintering in insects that is characterized by arrested development and increased tolerance to stress and cold. While the expression of specific candidate genes during diapause have been investigated, there is no general understanding of the dynamics of the transcriptional landscape as a whole during the extended diapause phenotype. Such a detailed temporal insight is important as diapause is a vital aspect of life cycle timing. Here, we performed a time-course experiment using RNA-Seq on the head and abdomen in the butterfly Pieris napi. In both body parts, comparing diapausing and nondiapausing siblings, differentially expressed genes are detected from the first day of pupal development and onwards, varying dramatically across these formative stages. During diapause there are strong gene expression dynamics present, revealing a preprogrammed transcriptional landscape that is active during the winter. Different biological processes appear to be active in the two body parts. Finally, adults emerging from either the direct or diapause pathways do not show large transcriptomic differences, suggesting the adult phenotype is strongly canalized.